Thanks for the added detail. You have a few things going on that make your system a bit tricky, but very fun
I remember you mentioned the "front yard gets the equivalent of 5.4 in per hour (minimum from 8 catch cups) on fixed spray heads" -- is this the same zone? I'm trying to understand the variance between 1.4 in per hour and 5.4 in per hour...maybe this was a typo?
This is a design error, but we can work around it. Could the head coverage be changed at all to avoid some of the overlap?
Was the supplement by rotor heads in zone (3) done to help with the drought? If so, I'd recommend adding a head to zone (2) and change the coverage pattern in zone (3).
We calculate the baseline watering times by factoring the vegetation type (how much water is needed) and divide over the precip rate of the nozzle (how much water is being applied). In your case, the precip rate is moving variable we need to figure out.
In regards to weather and avoiding runoff, these are best solved by lowering the threshold of your virtual rain sensor via the Weather Intelligence feature and enabled Smart Cycle. We can further adjust your Advanced Settings if needed to. Let me know your thoughts going forward.